Wednesday, June 24, 2009

We are happy to announce that STRING 8.1 has just been released. We have updated the interaction data, fixed a number of bugs and greatly improved the web interface. As always, we keep older versions around to guarantee reproducibility of earlier work (see here).

The interactive network viewer has been re-implemented (it's now based on Adobe Flash version 10), and it gives users the new opportunity to "play around" with the network while keeping the same look and feel as previously. The proteins in the network can now also be clustered, 'live', via two different methods: k-meansand markov chain clustering. The topology can be relaxed after clustering, or in real time by turning on "relaxation" and "cooling". The graph layouting is done by force-directed placement (see here), and the cooling is done by gradually lowering the relaxation variable hat determines the strength of node movements, to zero.Of course, this is merely a first version of the interactive viewer and future versions may well have additional features (in particular in case our users have specific requests).

We have also extended the protein structure previews. These are now not only based on PDB, but we also incorporate homology models from the SWISS-MODEL Repository. And, structure previews are finally shown in the proper context of the protein's domain architecture.

Lastly, we fixed several 'known issues' (i.e., bugs) - such as missing minor chromosomes for some species, and viewer problems with the textmining predictions.

To start playing with the new release, visit STRING 8.1 - and please don't hesitate to send us any feedback, criticism or suggestions...